QMRITools demonstration

The release and repository contains a demo data sets and a demonstration file in which there is a file Demonstrations.nb and a folder DemoData. If the tool has been installed as a paclet the paclet folder contains the Demonstrations.nb which will automatically unpack the demo data. By default the Demonstrations.nb looks for the folders DemoData in the same folder as the notebook.

To open the Demonstrations.nb open run the command OpenDemonstrationNotebook[] after installation and loading of the toolbox.

The Demonstrations.nb contains the following demonstrations.

Initialization

• Loading the toolbox definitions
• Verbose loading
• List all Packages and toolboxes
• Memory Usage

Basic Data manipulation and visualization

• Importing Data
• Plotting data Data
• Automatically find cross section images
• Rescaling Data
• Data Operations
  • Rotate data Dimensions
  • Remove singleton dimensions from data
  • Data array to vector
• Cropping
  • Automatic crop
  • Apply To Rescaled Data
  • Manual crop
  • Reverse the Crop
• Splitting Data
  • Split and Stitch
  • Example make both legs left
• Joining multiple stacks
  • Joining multiple data sets
  • Splitting joined data

General functions

• Define Data
• Filters
• Operation ignoring zeros

Masking

• Import Data
• Create Mask
  • Automated and threshold masking
  • Mask smoothing
  • Manual segmentation processing
  • Splitting segmentation in slice direction
  • Extract Data from Masks
• Rescaling Segmentations

Registration using Elastix

• Import Data
• Affine Transformation
• B-spline Registration of two legs
  • Full Registration
  • Constrained in one direction
• Register And Apply to other Data

Dixon and Phase unwrapping

• Simulated phase unwrapping
  • Simulate some Data
  • Unwrap simulated Data
• Dixon data
  • Import Data
  • Create a B0Map from phase data
  • Calculate a T2 star map from the echos
  • Perform iDeal reconstruction with initial B0 and T2star

Fasciculation Detection

• Import and select the Data
• Find and select activations
• Analyze and Evaluate activations

Simulate Dixon Data and fit testing

• Simulate the Dixon signal
• Fit the simulated Dixon signal
• Evaluate the fits

ME-SE (TSE) T2 mapping

• Import Data
• Define Slice Profiles
• calibrate and Fit the data

Simulate EPG Data and fit testing

• Simulate the EPG signal
• Fit the simulated EPG signal
• Evaluate the fits

DTI and IVIM

• Generating diffusion gradients
• Import The Data
• Prep the IVIM and DTI data
  • Sort and mask
  • Denoise DWI data
  • Motion and eddy current correction
• IVIM Fitting
  • Whole volume calibrate
  • IVIM fit
  • Split signals into perfusion and diffusion
• Tensor analysis
  • Fit the tensors
  • Analyze Tensor parameters
  • Calculate Tensor angles

Simulate Tensor Data and fit testing

• Simulate Diffusion signal
• Fit the simulated diffusion signal
• Evaluate the fits

Fiber Tractography

• Import The Data
• Process the data for tractography
• Fiber Tractography

J-coupling simulations

• Spin systems
  • Predefined spin systems
  • Custom spin systems
• Glutamate spectra with Steam
• Simulate Fat Spectra
  • PulseAcquire
  • Spin echo
  • STEAM
• Fat STEAM with various TEs

Cardiac data processing and simulation

• Simulate Cardiac Shape
• Analyze Cardiac shape
• Cardiac Segmentation
  • perform segmentation
  • Analyze data based on segmentation
  • Visualize results